The first mosque built in Delhi, the "Quwwat al-Islam" (near Qutb Minar) was built after the Jain temples built previously under the Tomara dynasty were forcefully converted into Mosques by the Muslim Sultanate.[2] 27 Jain temples were demolished to build this mosque whose name translates to "might of Islam". The remains of the temple were used for to provide the building material for the mosque.[3] Similarly the Jami Masjid at Khambhat was built on ruins of Jain temples.[4]

Muslims also destroyed many Jain holy sites during their rule in western India. They exerted serious pressure on the Jain community during 13th and 14th century.[7] Jains were powerless against the dominance of Islam at that time.[8]

Jinaprabha Suri (d.1333) writes in his "Vividhatirthakalpa" ("Guide to Various Pilgrimage Places") of his relationship with Muhammad bin Tughluq (r.1325-1351), Sultan of Delhi. In two chapters that discuss his relationship with the Sultan (one of which was actually written by his disciple), Jinaprabha travels to Delhi to recover an image that had been taken from a temple. After impressing the Sultan with his poetic flair and his thorough knowledge of the various religious and philosophical schools in India, the Sultan awards him with some blankets and other gifts, which Jinaprabha reluctantly accepts. In the second chapter, Jinaprabha is called back to Delhi to settle some religious matters for the Sultan. He is greeted warmly by the Sultan and even introduced to the Sultan's mother. One of his chief ministers is ordered to wipe the mud from Jinaprabha's feet. After getting the image back from the Sultan's treasury, Jinaprabha is paraded around the town on an elephant as a display of his pre-eminence in debate. He accompanies the Sultan on his military campaigns and upon his return is awarded a quarter of town in Tughluqabad for the Jain community, including a hall for Jinaprabha to teach in. Amid great fanfare and celebration the Jain community is declared by our author as prosperous and "just as when the Hindus ruled and times were not so bad, the glorious Jinaprabhasuri taught all those who come to him, even those of other faiths, and all rush to serve him."[9] Jinaprabha also secured edicts (firmans) to allow Jains to go on pilgrimage unharmed and untaxed (ibid.).

Under the leadership of Jinaprabha Suri and the Kharatara Gaccha, the Jains would remain an economically powerful and culturally vibrant community. While temples were desecrated, Jinaprabha speaks of these incidents as due to the power of the Dark Age (Kali Yuga) in which such things are going to happen. He also speaks of these desecrations as opportunities to earn "endless merit" by restoring temples, which laymen did with gusto.[10]

Some Jain customs and characters that influenced the Mughal court of Akbar have been documented. Akbar honored Hiravijaya, the leader of the SvetambaraTapa Gaccha.[11] They persuaded the emperor to forbid the slaughter of animals for six months in Gujarat and abolish the confiscation of property of deceased persons, the Sujija Tax (jizya) and a Sulka (possibly a tax on pilgrims) and free caged birds and prisoners. Akbar is said to have given up hunting and quit meat-eating forever as it had become repulsive.[11] Akbar also declared "Amari Ghosana" banning the killing of animals during Jain festival of Paryushana and Mahavira Jayanti. He rolled back the jizya from Jain pilgrimage places like Palitana. These farmans were also issued in 1592, 1594 and 1598.[11] Jain monks gained the respect of the Mughal emperors Jahangir [12] and Shah Jahan. Akbar banned animal slaughter near important Jain sites during the Paryushana.[13]

In 1645, the Mughal prince Aurangzeb desecrated the Chintamani Parshvanath Jain temple constructed by Shantidas Jhaveri, after being appointed the Governor of Gujarat. According to the French traveller Jean de Thévenot (1666), Aurangzeb caused a cow to be killed in the temple premises, destroyed the noses of all idols in the temple, and then converted the place into a mosque called Quvval-ul-Islam ("the Might of Islam").[14] Shantidas complained to Aurangzeb's father emperor Shah Jahan. In 1648, the Emperor issued a firman declaring that the building should be handed over to Shantidas, and a wall should be raised between the mihrabs (niches in the mosque walls) and the rest of the original temple building. It also declared that the Muslim fakirs housed in the mosque premises should be removed, and the materials carried away from the temple should be restored.[14][15]

As the Governor of Gujarat, Shah Jahan's son Murad Baksh granted the village of Palitana to Shantidas Jhaveri in 1656 which was a major pilgrimage centre of Jainism.[16]